What’s changed:

Bug Fixes

• This patch release resolves unintended typing of E. coli as Aeromonas and other organisms with similar alleles. When an E. coli sample was passed, alleles of Aeromonas could be called before identifying all of the alleles associated with E. coli, which can cause a mischaracterization as Aeromonas. Users can now usemlst_scheme_override to toggle on/off the exclusion of problematic allele sets with E. coli samples. By default, this behavior is turned off (”false”) because it is targeted for a specific use-case. We generally recommend users do not enable this option because it will overwrite the default sets excluded by ts_mlst. Please reach out if you would like to discuss this option.
• Reverted ts_mlst to not run both schemes for 3.1.0 in E. coli and A. baumannii by default*.* Previous release (v3.1.0) implemented a change to ts_mlst that by default enabled both schemes associated with E. coli and A. baumannii. While this behavior may still be desirable, we inadvertently introduced it in a way that users could not "opt in" to this functionality. Users can now decide if they wish to see single or double MLST scheme outputs in a single output column, using themlst_run_secondary_scheme boolean input. By default, this behavior is turned off (”false”).
• Fixes Mercury error where skip_ncbi was true for Mpox and GISAID metadata would not populate.

Other Updates

• The TheiaProk_Illumina Diagram is updated to include digger_denovo submodules.
• Samples_to_Ref_Tree is updated to include multiple genomes in a Nextclade phylogeny by accepting multiple samples as an input array.

User instructions:

• Change version to v3.1.1!
• Click “Use defaults” on the Outputs tab.

We treat patch releases just the same as major releases. You can feel confident knowing that we carefully validate the results to make sure there’s no unintended differences between versions.